RecG Bound to Three-Way DNA Junction

About this Structure
1GM5 is a 4 chains structure (1 protein chain and 3 nucleic acid chains) of sequences from Thermotoga maritima. Full crystallographic information is available from OCA.

The structure of RecG bound to a three-way junction is a monomeric protein  bound to 3 DNA chains  and adenosinediphosphate . [ This scene uses the DRuMS color scheme. ]

RecG has three structural domains :
 * The N-terminal domain, Domain 1, is about half the protein and extensively contacts the DNA junction.
 * Domain 2 is one of the two RecA-like domains common to helicases/translocases;  ADP  is bound here.
 * Domain 3 is the other of the two RecA-like domains common to helicases/translocases.

Schematic of the DNA fork seen in the structure:

Structural motifs of domain 1 :
 * N-terminal helical subdomain.
 * The wedge subdomain, this orientation better shows how this subdomain splits the arms of the junction. Grooves on the sides of the wedge are too narrow to accommodate duplex DNA
 * The remainder of domain 1.

Further details of the interaction between the protein and junction :
 * The protein is shown in silver to enable highlighting of significant features.
 * Phe204 and Tyr208 stack on the orphan bases to stabilize and cap the helical regions at the junction.
 * A base that was paired in the original substrate is flipped out in the structure as it seems to be caught in the middle of switching between duplexes of the fork and presumably this base isn't stabilized in keeping with it being a transient state.

Surface representation of the interaction with the DNA substrate. [ Note: this view generates a substantial surface which may take several minutes to calculate. Be patient. ]
 * This scene probably most clearly shows that grooves on the sides of the wedge are too narrow to accommodate duplex DNA.
 * Presumably if the template duplex arm were longer as it would be in vivo, it would interact with domains 2 and 3, perhaps in the cleft between them.

Additional Resources
For additional information, see: DNA Replication, Repair, and Recombination

Reference
Categor: Topic Page

Page originally seeded by OCA on Mon Feb 16 22:17:57 2009